Two unique chicken F2 populations generated from a broiler breeder male line and 2 genetically distinct inbred (>99%) chicken lines (Leghorn and Fayoumi) were used for whole genome QTL analysis. Twelve phenotypic skeletal integrity traits (6 absolute and 6 relative traits) were measured or calculated, including bone mineral content, bone mineral density, tibia length, shank length, shank weight, and shank length:shank weight. All traits were also expressed as a percentage of BW at 8 wk of age. Birds were genotyped for 269 microsatellite markers across the entire genome. The QTL affecting bone traits in chickens were detected by the QTL express program. Significance levels were obtained using the permutation test. For the 12 traits, a total of 56 significant QTL were detected at the 5% chromosome-wise significance level, of which 14 and 10 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Phenotypic variation for each trait explained by all detected QTL across the genome ranged from 12.0 to 35.6% in the broiler-Leghorn cross and 2.9 to 31.3% in the broiler-Fayoumi cross. Different QTL profiles identified between the 2 related F2 crosses for most traits suggested that genetic background is an important factor for QTL analysis. Study of associations of biological candidate genes with skeletal integrity traits in chickens will reveal new knowledge of understanding biological process of skeletal homeostasis. The results of the current study have identified markers for bone strength traits, which may be used to genetically improve skeletal integrity in chickens by MAS, and to identify the causal genes for these traits.